Molecular Biology 5th Edition
One of my most exciting educational experiences was my introductory molecular biology course in graduate school. My professor used no textbook, but assigned us readings directly from the scientifi c literature. It was challenging, but I found it immensely satisfying to meet the challenge and understand, not only the conclusions, but how the evidence supported those conclusions.
When I started teaching my own molecular biology course, I adopted this same approach, but tried to reduce the challenge to a level more appropriate for undergraduate students. I did this by narrowing the focus to the most important experiments in each article, and explaining those carefully in class. I used hand-drawn cartoons and photocopies of the fi gures as illustrations.
This approach worked well, and the students enjoyed it, but I really wanted a textbook that presented the concepts of molecular biology, along with experiments that led to those concepts. I wanted clear explanations that showed students the relationship between the experiments and the concepts. So, I finally decided that the best way to get such a book would be to write it myself. I had alreadycoauthored a successful introductory genetics text in which I took an experimental approach—as much as possible with a book at that level. That gave me the courage to try writing an entire book by myself and to treat the subject as an adventure in discovery.
The book begins with a four-chapter sequence that should be a review for most students. Chapter 1 is a brief history of genetics. Chapter 2 discusses the structure and chemical properties of DNA. Chapter 3 is an overview of gene expression, and Chapter 4 deals with the nuts and bolts of gene cloning. All these are topics that the great majority of molecular biology students have already learned in an introductory genetics course. Still, students of molecular biology need to have a grasp of these concepts and may need to refresh their understanding of them. I do not deal specifically with these chapters in class; instead, I suggest students consult them if they need more work on these topics. These chapters are written at a more basic level than the rest of the book.
Chapter 5 describes a number of common techniques used by molecular biologists. It would not have been possible to include all the techniques described in this book inone chapter, so I tried to include the most common or, in a few cases, valuable techniques that are not mentioned elsewhere in the book. When I teach this course, I do not present Chapter 5 as such. Instead, I refer students to it when we fi rst encounter a technique in a later chapter. I do it that way to avoid boring my students with technique after technique. I also realize that the concepts behind some of these techniques are rather sophisticated, and the students’ appreciation of them is much deeper after they’ve acquired more experience in molecular biology.
Chapters 6–9 describe transcription in bacteria. Chapter 6 introduces the basic transcription apparatus, including promoters, terminators, and RNA polymerase, and shows how transcripts are initiated, elongated, and terminated. Chapter 7 describes the control of transcription in three different operons, then Chapter 8 shows how bacteria and their phages control transcription of many genes at a time, often by providing alternative sigma factors. Chapter 9 discusses the interaction between bacterial DNAbinding proteins, mostly helix-turn-helix proteins, and their DNA targets.
Chapters 10–13 present control of transcription in eukaryotes. Chapter 10 deals with the three eukaryotic RNA polymerases and the promoters they recognize. Chapter 11 introduces the general transcription factors that collaboratewith the three RNA polymerases and points out the unifying theme of the TATA-box-binding protein, which participates in transcription by all three polymerases. Chapter 12 explains the functions of gene-specifi c transcription factors, or activators. This chapter also illustrates the structures of several representative activators and shows how they interact with their DNA targets. Chapter 13 describes the structure of eukaryotic chromatin and shows how activators and silencers can interact with coactivators and corepressors to modify histones, and thereby to activate or repress transcription.
Chapters 14–16 introduce some of the posttranscriptional events that occur in eukaryotes. Chapter 14 deals with RNA splicing. Chapter 15 describes capping and polyadenylation, and Chapter 16 introduces a collection of fascinating “other posttranscriptional events,” including rRNA and tRNA processing, trans-splicing, and RNA editing. This chapter also discusses four kinds of posttranscriptional control of gene expression: (1) RNA interference; (2) modulating mRNA stability (using the transferrin receptor mRNA as the prime example); (3) control by microRNAs, and (4) control of transposons in germ cells by Piwi-interacting RNAs (piRNAs).
About the Author iv
Guide to Experimental Techniques in
Molecular Biology xix
1 A Brief History 1
2 The Molecular Nature of Genes 12
3 An Introduction to Gene Function 30
PART I I
Methods in Molecular Biology
4 Molecular Cloning Methods 49
5 Molecular Tools for Studying Genes and Gene
PART I I I
Transcription in Bacteria
6 The Mechanism of Transcription in Bacteria 121
7 Operons: Fine Control of Bacterial
8 Major Shifts in Bacterial Transcription 196
9 DNA–Protein Interactions in Bacteria 222
PART I V
Transcription in Eukaryotes
10 Eukaryotic RNA Polymerases and
Their Promoters 244
11 General Transcription Factors
in Eukaryotes 273
12 Transcription Activators in Eukaryotes 314
13 Chromatin Structure and Its Effects
on Transcription 355
14 RNA Processing I: Splicing 394
15 RNA Processing II: Capping and Polyadenylation 436
16 Other RNA Processing Events and Post-Transcriptional
Control of Gene Expression 471
PART V I
17 The Mechanism of Translation I: Initiation 522
18 The Mechanism of Translation II: Elongation
and Termination 560
19 Ribosomes and Transfer RNA 601
PART V I I
DNA Replication, Recombination,
20 DNA Replication, Damage, and Repair 636
21 DNA Replication II: Detailed Mechanism 677
22 Homologous Recombination 709
23 Transposition 732
PART V I I I
24 Introduction to Genomics: DNA Sequencing on
a Genomic Scale 759
25 Genomics II: Functional Genomics, Proteomics,
and Bioinformatics 789
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